Gene detail

Detailed information of OS493_017855-T1 in Lophelia pertusa

Genomic Location: scaffold_58:137313...141356
NR annotation: KAJ7372584.1, translation initiation factor eIF-3b like protein [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q4G061	Eukaryotic translation initiation factor 3 subunit B OS=Rattus norvegicus OX=10116 GN=Eif3b PE=1 SV=1
Q8JZQ9	Eukaryotic translation initiation factor 3 subunit B OS=Mus musculus OX=10090 GN=Eif3b PE=1 SV=1
P55884	Eukaryotic translation initiation factor 3 subunit B OS=Homo sapiens OX=9606 GN=EIF3B PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006577 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR011400 all species →	Family	Eukaryotic translation initiation factor 3 subunit B	Interproscan
IPR034363 all species →	Domain	eIF3B, RNA recognition motif	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14068 all species →	EUKARYOTIC TRANSLATION INITIATION FACTOR 3 EIF3 -RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003743 all species →	Molecular Function	translation initiation factor activity	Interproscan
GO:0005852 all species →	Cellular Component	eukaryotic translation initiation factor 3 complex	Interproscan
GO:0006413 all species →	Biological Process	translational initiation	Interproscan
GO:0031369 all species →	Molecular Function	translation initiation factor binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K12876	RBM8A, Y14; RNA-binding protein 8A	-	Spliceosome	ko03041	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_017855-T1 across 110 RNA-seq samples of Lophelia pertusa. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

110Samples

110TPM > 0

7Conditions

195.6Max TPM

69.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	40.02	67.31
polyp at pH7 6	18	18	50.18	68.84
coral polyp · control treatment	16	16	93.05	150.99
coral polyp · oil and dispersant treatment	16	16	105.17	195.59
coral polyp · oil treatment	16	16	74.98	162.42
coral polyp · dispersant treatment	16	16	80.08	157.51
Polyp	10	10	36.37	69.59

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	67.31
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.05
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.16
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.38
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.05
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.05
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.80
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.54
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.11
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.84
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.29
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.15
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.24
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.88
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.00
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.99
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.81
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.74
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.84
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.89
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.22
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.75
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.64
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.04
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.81
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.33
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.73
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.01
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.08
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.32
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.55
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.71
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.57
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.75
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.77
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.23
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	150.99
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	147.15
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	143.16
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	127.36
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	113.40
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	95.88
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	91.18
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	82.25
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	81.67
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	81.18
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	78.70
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	74.97
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	69.50
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.19
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.52
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.70
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	195.59
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	150.36
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	130.14
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	130.01
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	122.10
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	118.35
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	114.06
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	99.53
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	96.42
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	82.75
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.81
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	79.40
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	77.62
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	74.34
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	71.06
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.16
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	162.42
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	97.91
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	95.38
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	87.80
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	86.12
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	85.35
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	81.98
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	80.43
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	72.79
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	70.86
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	69.54
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.52
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.99
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.16
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.89
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.53
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	157.51
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	118.19
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	113.09
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	112.26
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	106.42
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	94.52
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	88.66
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	85.67
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	75.26
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	65.80
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.49
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.42
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.50
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.58
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.35
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.50
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	69.59
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	63.71
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	42.18
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	31.60
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	31.44
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	31.17
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	29.00
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	26.67
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	22.00
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	16.31

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.